readsEndPlot {ribosomeProfilingQC} | R Documentation

## Plot start/stop windows

### Description

Plot the reads shifted from start/stop position of CDS.

### Usage

    readsEndPlot(
      bamfile,
      CDS,
      toStartCodon = TRUE,
      fiveEnd = TRUE,
      shift = 0,
      window = c(-29, 30),
      readLen = 25:30
    )

### Arguments

`bamfile` | A BamFile object.
`CDS` | Output of prepareCDS
`toStartCodon` | What to search: start or end codon
`fiveEnd` | Search from five or three ends of the reads.
`shift` | number(1). Search from 5' end or 3' end of given number. if fiveEnd set to false, please set the shift as a negative number.
`window` | The window of CDS region to plot
`readLen` | The reads length used to plot

### Value

The invisible counts numbers.

### Examples

    library(Rsamtools)
    bamfilename <- system.file("extdata", "RPF.WT.1.bam",
                               package="ribosomeProfilingQC")
    yieldSize <- 10000000
    bamfile <- BamFile(bamfilename, yieldSize = yieldSize)
    #library(GenomicFeatures)
    library(BSgenome.Drerio.UCSC.danRer10)
    #txdb <- makeTxDbFromGFF(system.file("extdata",
     #         "Danio_rerio.GRCz10.91.chr1.gtf.gz",
     #         package="ribosomeProfilingQC"),
     #         organism = "Danio rerio",
     #         chrominfo = seqinfo(Drerio)["chr1"],
     #         taxonomyId = 7955)
    #CDS <- prepareCDS(txdb)
    CDS <- readRDS(system.file("extdata", "CDS.rds",
                               package="ribosomeProfilingQC"))
    readsEndPlot(bamfile, CDS, toStartCodon=TRUE)
    #readsEndPlot(bamfile, CDS, toStartCodon=TRUE, fiveEnd=FALSE)
    #readsEndPlot(bamfile, CDS, toStartCodon=FALSE)
    #readsEndPlot(bamfile, CDS, toStartCodon=FALSE, fiveEnd=FALSE)
    readsEndPlot(bamfile, CDS, shift=13)
    #readsEndPlot(bamfile, CDS, fiveEnd=FALSE, shift=-16)

[Package ribosomeProfilingQC version 0.99.9 Index]